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- PDB-6w3v: Crystal structure of ligand-binding domain of Campylobacter jejun... -

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Basic information

Entry
Database: PDB / ID: 6w3v
TitleCrystal structure of ligand-binding domain of Campylobacter jejuni chemoreceptor Tlp3 in complex with L-phenylalanine
ComponentsMethyl-accepting chemotaxis protein
KeywordsSIGNALING PROTEIN / Bacterial chemotaxis / chemoreceptor / double Cache / ligand binding domain
Function / homology
Function and homology information


membrane => GO:0016020 / signal transduction / membrane
Similarity search - Function
Methyl-accepting chemotaxis protein-like, first PDC sensor domain / Double Cache domain 1 / Cache domain / Periplasmic sensor-like domain superfamily / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / PAS domain / Beta-Lactamase ...Methyl-accepting chemotaxis protein-like, first PDC sensor domain / Double Cache domain 1 / Cache domain / Periplasmic sensor-like domain superfamily / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / PAS domain / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHENYLALANINE / Methyl-accepting chemotaxis protein / Methyl-accepting chemotaxis signal transduction protein
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsKhan, M.F. / Machuca, M.A. / Rahman, M.M. / Roujeinikova, A.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: Biomolecules / Year: 2020
Title: Structure-Activity Relationship Study Reveals the Molecular Basis for Specific Sensing of Hydrophobic Amino Acids by theCampylobacter jejuniChemoreceptor Tlp3.
Authors: Khan, M.F. / Machuca, M.A. / Rahman, M.M. / Koc, C. / Norton, R.S. / Smith, B.J. / Roujeinikova, A.
History
DepositionMar 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1May 27, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methyl-accepting chemotaxis protein
B: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0179
Polymers57,4012
Non-polymers6167
Water13,655758
1
A: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0935
Polymers28,7001
Non-polymers3934
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9244
Polymers28,7001
Non-polymers2243
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-62 kcal/mol
Surface area24320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.396, 137.359, 48.759
Angle α, β, γ (deg.)90.000, 93.960, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Methyl-accepting chemotaxis protein


Mass: 28700.498 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: D8X59_02240 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3X8N4T9, UniProt: Q0P864*PLUS

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Non-polymers , 5 types, 765 molecules

#2: Chemical ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 758 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, sodium citrate and ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.38→45.852 Å / Num. obs: 96443 / % possible obs: 98.7 % / Redundancy: 3.2 % / Biso Wilson estimate: 17.84 Å2 / Rmerge(I) obs: 0.032 / Net I/σ(I): 12.4
Reflection shellResolution: 1.38→1.4 Å / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4xmr

4xmr


Resolution: 1.47→45.852 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 12.03
RfactorNum. reflection% reflection
Rfree0.1479 4628 4.98 %
Rwork0.1357 --
obs0.1364 92852 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 142.57 Å2 / Biso mean: 28.0901 Å2 / Biso min: 9.23 Å2
Refinement stepCycle: final / Resolution: 1.47→45.852 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3943 0 37 758 4738
Biso mean--32.43 43.01 -
Num. residues----495
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134219
X-RAY DIFFRACTIONf_angle_d1.3565759
X-RAY DIFFRACTIONf_chiral_restr0.11665
X-RAY DIFFRACTIONf_plane_restr0.015747
X-RAY DIFFRACTIONf_dihedral_angle_d13.6531584
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.47-1.48670.18551560.20152965100
1.4867-1.50420.20761620.19032949100
1.5042-1.52250.19971860.18163001100
1.5225-1.54180.18221500.17162870100
1.5418-1.56210.18011970.16443007100
1.5621-1.58350.15991430.15372971100
1.5835-1.60610.16461460.1482975100
1.6061-1.63010.12851430.14313021100
1.6301-1.65560.13261650.13032903100
1.6556-1.68270.13961520.13223042100
1.6827-1.71170.14791450.13052942100
1.7117-1.74290.15441610.1232971100
1.7429-1.77640.1421550.13172991100
1.7764-1.81270.15761430.14642985100
1.8127-1.85210.16261600.1412965100
1.8521-1.89520.14361750.13332958100
1.8952-1.94250.12861410.1236297399
1.9425-1.99510.12421420.12712969100
1.9951-2.05380.1161660.1136294899
2.0538-2.12010.14021600.1182296999
2.1201-2.19580.12291340.1189293999
2.1958-2.28380.13891490.1227295499
2.2838-2.38770.1211320.1212299399
2.3877-2.51360.13111550.1261295399
2.5136-2.6710.12981420.1256296199
2.671-2.87720.15481420.1317296498
2.8772-3.16670.14471640.1355291698
3.1667-3.62480.14811710.1326287397
3.6248-4.56620.15221490.1355276392

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